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Simulating DNA to tackle tough medical challenges

Researchers at IU are making advances in studying DNA to tackle considerable challenges.

Dr. Robert Molt Jr., a postdoctoral researcher in the Department of Chemistry and Chemical Biology at IUPUI and Department of Biochemistry and Molecular Biology at the Indiana University School of Medicine, has been conducting exciting new health-related research using IU’s advanced cyberinfrastructure resources including Big Red II and Karst. Much of his work centers on the protein biochemistry mechanisms involved in cancer and generating artificial DNA nucleotides. According to Dr. Molt, “understanding how proteins work regarding cancer enables us to screen for inhibitors that can save lives.” He also added that his work with artificial DNA allows for a deeper understanding of genetics and that his hope was to develop (stable) artificial genes to help people with genetic defects.

DNA - Dipole Moments

Dipole moments and the ESP for different nucleobase pairs

One of the toughest challenges that Dr. Molt and other scientist face is access to advanced computing facilities. Dr. Molt’s work involves simulating DNA helices every 2x10-15 seconds of time for a total time of 5x10-5 seconds  (i.e., 10 orders of magnitude in time!). According to Dr. Molt, “computing a dynamically stable trajectory over 10 orders of magnitude in time is only possible using the many GPUs of IU. I have been able to utilize ~150 GPUs at a time to achieve such calculations.”